[BioC] Coverage of reads per base position from BAM files

[Mukherjee, Rithun]

Thanks very much, it worked!

Regards,
Rithun

----- Original Message -----
From: "Michael Lawrence" <lawrence.michael at gene.com>
To: "Rithun Mukherjee [guest]" <guest at bioconductor.org>
Cc: bioconductor at r-project.org, rmukherj at fhcrc.org, "Rsamtools Maintainer" <maintainer at bioconductor.org>
Sent: Tuesday, July 17, 2012 2:11:33 PM
Subject: Re: [BioC] Coverage of reads per base position from BAM files

You can readGappedAlignments to load the file as a GappedAlignments. Then call coverage() on that. 

Michael 


On Tue, Jul 17, 2012 at 12:56 PM, Rithun Mukherjee [guest] < guest at bioconductor.org > wrote: 



I am trying to obtain per reference base position coverage for a BAM file. The BAM file has been generated by Samtools and contains alignment info for 10 million reads to a 7kb reference plasmid genome. What is the best way to go about this? I have explored the "readBamGappedAlignments" and "readAligned" functions but I am not sure of the way forward from there. 

Also should I be using a BAM file or the sorted BAM file with its corresponding index file? I am currently using the later. 

Thanks much. 


-- output of sessionInfo(): 

R version 2.14.2 (2012-02-29) 
Platform: x86_64-unknown-linux-gnu (64-bit) 

locale: 
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 
[7] LC_PAPER=C LC_NAME=C 
[9] LC_ADDRESS=C LC_TELEPHONE=C 
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 

attached base packages: 
[1] stats graphics grDevices utils datasets methods base 

other attached packages: 
[1] ShortRead_1.12.4 latticeExtra_0.6-19 RColorBrewer_1.0-5 
[4] lattice_0.20-6 Rsamtools_1.6.3 Biostrings_2.22.0 
[7] GenomicRanges_1.6.7 IRanges_1.12.6 

loaded via a namespace (and not attached): 
[1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 grid_2.14.2 
[5] hwriter_1.3 RCurl_1.91-1 rtracklayer_1.14.4 tools_2.14.2 
[9] XML_3.9-4 zlibbioc_1.0.1 


-- 
Sent via the guest posting facility at bioconductor.org . 

_______________________________________________ 
Bioconductor mailing list 
Bioconductor at r-project.org 
https://stat.ethz.ch/mailman/listinfo/bioconductor 
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor 

-- 
Rithun Mukherjee
Postdoctoral Research Associate
Computational Biology Program
Fred Hutchinson Cancer Research Center

rmukherj at fhcrc.org
206.667.7661